Kondo2014Nakamura
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JournalofMolecularCatalysisB:Enzymatic110(2014)23–31
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JournalofMolecularCatalysisB:
Enzymatic
journalhomepage:www.elsevier.com/locate/molcatb
AsignificantroleofArg41residueintheenzymaticreactionof
haloaciddehalogenasel-DEXYLstudiedbyQM/MMmethod
HirotakaKondoa,∗,TakashiNakamurab,ShigenoriTanakac,∗
aGraduateSchoolofHumanDevelopmentandEnvironment,KobeUniversity,3-11Tsurukabuto,Nada,Kobe657-8501,JapanbNagahamaInstituteofBio-ScienceandTechnology,1266Tamura,Nagahama,Shiga526-0829,JapancGraduateSchoolofSystemInformatics,KobeUniversity,1-1Rokkodai,Nada,Kobe657-8501,Japan
articleinfo
Articlehistory:Received7April2014Receivedinrevisedform23August2014Accepted12September2014Availableonline22September2014
Keywords:Enzymaticreaction2-Haloaciddehalogenasel-2-ChloropropionicacidONIOMmethodTransitionstateabstract
l-2-Haloaciddehalogenase(l-DEX)isoneofafamilyofenzymesthatdecomposeavarietyofenvi-ronmentalpollutantssuchasl-2-chloropropionate(l-2-CPA).Thisenzymespecificallyproducesad-2-hydroxyacidfromal-2-haloacid,and,todate,someresidueshavebeensuggestedasimportantinthisenzymaticreaction.Here,quantum-mechanical(QM)/molecular-mechanical(MM)calculationsforthel-DEXfromPseudomonassp.YL(l-DEXYL)2-CPAcomplexwereperformedtoelucidatethestruc-tureoftransitionstateandtheenergyprofileinthisenzymaticreaction.QM/MMsimulationsusingtheONIOM(PM3:Amber)methodrevealedthattheactivationenergyofdehalogenationreactionwasaround9.0kcal/molandthatoneofthemostimportantresiduesintheesterintermediateformationstepwasArg41,whichwasfoundtodecreasetheactivationenergybyabout40kcal/molcomparedtothecaseofitsabsence.Ontheotherhand,thisstabilizationeffectbyArg41wassignificantlycounterbalancedbythepresenceofAsn177.SimulationsofenzymesmutatedatArg41indicatedthatmutantspossessingapositivechargeneartheArg41positionwouldallowthedehalogenationreactionaswell.Specifically,itwassuggestedbyoursimulationsthathomolysine(homK)mutantofArg41,whichcontainsonemoremethylenegroupinthesidechaincomparedtolysine,couldbeactiveaswellasthewild-typeenzyme.Thedistancefromthechlorideiontothepositionofthepositivechargeoftheacceptorseemstodictatetheactivationenergy.©2014ElsevierB.V.Allrightsreserved.
1.Introduction
Manyorganohalogencompoundsareknowntobeproduced
biologicallyorbynaturalabiogenicprocesses[1].Producedin
largequantitiesbythechemicalindustryduetotheirusefulness
assolvents,pharmaceuticals,andagrochemicals,thesechemicals
alsocauseseriousenvironmentalpollutionandhealthproblems.
Dehalogenasesdetoxifyvarioushalogencompounds,catalyzing
theremovalofahalogenatomfromtheirsubstrates,andareuse-
fulinenvironmentaltechnologytodecontaminateenvironments
pollutedwithharmfulorganohalogencompounds.
2-Haloaciddehalogenaseshavebeenextensivelystudiedand
reviewed[2,3].Onedehalogenase,l-2-haloaciddehalogenase(l-
DEX),catalyzesthehydrolyticdehalogenationofl-2-haloalkanoic
acidstoproducethecorrespondingd-2-hydroxyalkanoicacids
∗Correspondingauthors.Tel.:+810788036620;fax:+810788036621.E-mailaddresses:kondo@eniac.scitec.kobe-u.ac.jp(H.Kondo),tnakamura@nagahama-i-bio.ac.jp(T.Nakamura),tanaka2@kobe-u.ac.jp(S.Tanaka).withthereleaseofhalideions.Arepresentativeenzymeofthe
haloaciddehalogenasesuperfamily,l-DEX,hasbeenisolatedand
purifiedfromseveralmicrobialstrains[4].l-DEXYLwasisolated
fromPseudomonassp.strainYLcellcultureinamediumcontaining
2-chloropropionate(2-CPA)asthesolecarbonsource[5].Thereac-
tionmechanismsofl-DEXYLhavebeenanalyzedbysite-directed
mutagenesis[6],X-raycrystallography[7–9],massspectrometry
[10–12],18O-incorporationexperiments[13],andcomputersimu-
lationsbythemoleculardynamicsandfragmentmolecularorbital
methods[14].
Site-directedmutagenesisexperimentshaverevealedthat
thoseaminoacidresiduessuchasAsp10,Thr14,Arg41,Ser118,
Lys151,Tyr157,Ser175,Asn177andAsp180areimportantforthe
catalyticfunctionofl-DEXYL[6].18O-incorporationexperiments
haverevealedthatAsp10playsapivotalroleinanucleophilic
attackonasubstrate˛-carbontoformanesterintermediate,
whichisthenhydrolyzedbywater[13].Thesestudiessuggestthe
reactionmechanismshowninFig.1.Massspectrometryanalysis
hasshowntheinvolvementofArg41andAsp180intheformation
ofanesterintermediate[12].X-raycrystallographicanalysisof
l-DEXYLhasprovidedfurtherevidencefortheformationofan
http://dx.doi.org/10.1016/j.molcatb.2014.09.0061381-1177/©2014ElsevierB.V.Allrightsreserved.24H.Kondoetal./JournalofMolecularCatalysisB:Enzymatic110(2014)23–31
Fig.1.Thereactionmechanismofl-DEXYL.l-2-haloaciddehalogenasescatalyzehydrolyticdehalogenationofl-2-haloalkanoicacidstoproducecorrespondingd-2-hydroxyalkanoicacidswithreleaseofhalideion.XandRmeanhalogenandalkylgroupincludinghydrogen,respectively.
esterintermediateandinformationonthefunctionsofactive-site